X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3bc9bc56f33848ec04e901519cc1d0199fb423fd;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=3bfc7db208167d24399600f1dc45066af77ad169;hpb=3d2554c478e12c745b1270edd21daeef03de636c;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3bfc7db..3bc9bc5 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -115,8 +115,7 @@ public class SeqPanel extends JPanel
 
     seqEditOccurred = -1;
 
-    ap.RefreshPanels();
-    repaint();
+    ap.repaint();
 
   }
 
@@ -420,14 +419,9 @@ public class SeqPanel extends JPanel
       stretchGroup = sg;
 
       if(av.getConservationSelected())
-        Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())
-      {
-        ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();
-        int threshold = rcs.getThreshold();
-        if (threshold > 0)
-          Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
-      }
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      if(av.getAbovePIDThreshold())
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
 
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
@@ -472,13 +466,9 @@ public class SeqPanel extends JPanel
 
     else if(stretchGroup.cs instanceof ConservationColourScheme)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
-
-
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
        stretchGroup.cs = ccs;
-
-
-       Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
 
        repaint();
     }
@@ -487,9 +477,7 @@ public class SeqPanel extends JPanel
       if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
       {
         ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
-        int threshold = rcs.getThreshold();
-        if(threshold>0)
-          Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
       }
 
     }
@@ -511,8 +499,8 @@ public class SeqPanel extends JPanel
     if(stretchGroup==null)
       return;
 
-    if(res>av.alignment.getWidth()-2)
-      res = av.alignment.getWidth()-2;
+    if(res>av.alignment.getWidth())
+      res = av.alignment.getWidth()-1;
 
 
     if(stretchGroup.getEndRes()==res)